SLE is a clinically heterogenous, challenging to evaluate autoimmune disease. Improved objective standards for global assessment of disease activity and evaluation of therapeutic interventions are needed. In addition, individualized measures of organ-specific damage should be defined as they could lead to the identification of predictors to implement earlier therapeutic interventions and prevent irreversible damage. Thus, there is an important need to develop objective, simple and robust SLE biomarkers. Pediatric and adult SLE patients display unique blood biosignatures that reflect the alterations in cellular and cytokine pathways that contribute to disease pathogenesis. These biosignatures can be used to assess disease activity. Most adult lupus studies have focused on the use of IFN alpha-induced transcripts and/or proteins as biomarkers of disease activity. IFN activity, however, has been shown to decrease in lupus patients with age, underscoring the need for more global approaches to identify useful lupus biomarkers that can be used in all age groups. We have developed a series of genomic and bioinformatics tools that allow the systematic evaluation of robust blood transcriptionahmodules displaying unique behaviors in patients with immune mediated diseases, including SLE. Transcriptionally co-regulated genes span not only those induced by type I IFN, but also those derived from a broader array of cell types and biological pathways. Genomic scores obtained using simple multivariate analysis that integrate several of these transcriptional modules perform well in longitudinal studies of pediatric SLE patients compared to validated disease activity measures. We now propose to establish a reference database for the assessment of SLE disease activity in adults using genomic scoring. We will next design a state of the art inexpensive and focused lupus microarray for monitoring patients in the clinical setting. Our objectives are 1) to establish and follow a longitudinal cohort of adult SLE and CLE patients, 2) to identify transcriptional markers for the assessment of disease activity and organ damage in these patients, with the ultimate goal of 3) designing and validating a cost-effective and practical assay for monitoring patients in the clinical setting.